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Add GARD alignments, batchfiles, output.
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sidneymbell
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Jan 10, 2017
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recombination/gard/windowA/lanl14_lesshiv_A.fasta
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| <!DOCTYPE HTML PUBLIC '-//W3C//DTD HTML 4.01 Transitional//EN'><html><head><META http-equiv='Content-Style-Type' content='text/css'><meta http-equiv='Content-Type' content='text/html; charset=ISO-8859-1'><title>GARD Results</title><LINK REL=STYLESHEET TYPE='text/css' HREF='http://www.datamonkey.org/GARD/styles/styles.css'></head><body><DIV CLASS = 'RepClassSM'>Processed alignment <b>/home/sbell23/gardA/lanl14_lesshiv_A.fasta</b> with 64 sequences and 3000 sites.<p> Processor time taken: 52623 seconds.</DIV><DIV class = 'RepClassSM'><u>Results</u><p><DIV class = 'RepClassSM'><b>GARD found evidence of 1 breakpoints</b><p><html><body><div style = 'width: 580px; border: black solid 1px; '><table style = 'width: 100%;font-size: 10px;text-align:left;'><tr><th>BPs</th><th>c-AIC</th><th>Δ c-AIC</th><th width = '70%'>Segments</th></tr> | ||
| <tr><td>0</td><td><div style = 'width: 100%; background-color: purple; color: white;'>165590.5405143086</div></td><td></td><td><table><tr><td style = 'font-size:10px;width: 406px;background-color:red; color:white'>1-3000</td></tr></table></td></tr> | ||
| <tr><td>1</td><td><div style = 'width: 99%; background-color: purple; color: white;'>165234.274687486</div></td><td>356.2658268226078</td><td><table style = 'padding: 0px; spacing: 0px;'><tr><td style = 'width:321px; background-color: red; color: white; text-align: right; font-size: 10px;'>2373</td><td style = 'width:84px; background-color: black; color: white; text-align: right; font-size: 10px;'> </td></tr></table></td></tr> | ||
| <tr><td>2</td><td><div style = 'width: 99%; background-color: purple; color: white;'>165234.274687486</div></td><td>0</td><td><table style = 'padding: 0px; spacing: 0px;'><tr><td style = 'width:321px; background-color: red; color: white; text-align: right; font-size: 10px;'>2373</td><td style = 'width:84px; background-color: black; color: white; text-align: right; font-size: 10px;'> </td></tr></table></td></tr> | ||
| </table></div></body></html></DIV> | ||
| </DIV><DIV CLASS='RepClassSM'><span class = 'font-variant:small-caps;'>Substitution process parameters</span><p><b>Nucleotide Model (012234) Fit Results</b><p>Log likelihood : <span style = 'position: absolute; left: 290px'>-82652.76239826504</span><br>c-AIC : <span style = 'position: absolute; left: 290px'>165590.5405143086</span><br><p>Using general discrete distribution of rates across sites<br> Rate : 0.058<span style = 'position: absolute; left: 290px'>Weight : 0.185</span><br> Rate : 0.523<span style = 'position: absolute; left: 290px'>Weight : 0.263</span><br> Rate : 1.542<span style = 'position: absolute; left: 290px'>Weight : 0.552</span><p><u>Nucleotide substitution rate matrix</u><p><TABLE><TR CLASS = 'TRReportT'><TH> </TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR><TR CLASS = 'TRReport1'><TH>A</TH><TD>*</TD><TD>0.4832270840810896</TD><TD>1</TD><TD>0.4625754663045142</TD></TR><TR CLASS = 'TRReport2'><TH>C</TH><TD>-</TD><TD>*</TD><TD>0.4625754663045142</TD><TD>1.116637626049968</TD></TR><TR CLASS = 'TRReport1'><TH>G</TH><TD>-</TD><TD>-</TD><TD>*</TD><TD>0.2505550635176408</TD></TR><TR CLASS = 'TRReport2'><TH>T</TH><TD>-</TD><TD>-</TD><TD>-</TD><TD>*</TD></TR></TABLE></DIV></html></body></html> |
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| inputRedirect = {}; | ||
|
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| /* specify input alignment (full path) */ | ||
| inputRedirect["01"]="/home/sbell23/gardA/lanl14_lesshiv_A.fasta"; | ||
|
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| /* specify nucleotide model (perhaps run NucModelCompare, or use GTR=012345 */ | ||
| inputRedirect["02"]="012234"; | ||
|
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| /* site variation? General Discrete is recommended, but other options are None (fastest) or Beta-Gamma */ | ||
| inputRedirect["03"]="General Discrete"; | ||
|
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| /* How many distribution bins [2-32]? (unless None was chosen for site variation, in which case do not use this input) */ | ||
| inputRedirect["04"]="3"; | ||
|
|
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| /* specify what output files will be called - there will be four outputs, with this stem in the name (give full path, otherwise it'll end up in /home/jayoung/malik_lab_shared/linux_gizmo/lib/hyphy/TemplateBatchFiles) */ | ||
| inputRedirect["05"]="/home/sbell23/gardA/lanl14_lesshiv_A.fasta.GARD"; | ||
|
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| /* do the analysis */ | ||
| ExecuteAFile (HYPHY_BASE_DIRECTORY + DIRECTORY_SEPARATOR+"GARD.bf", inputRedirect); |
3,328 changes: 3,328 additions & 0 deletions
3,328
recombination/gard/windowB/lanl14_lesshiv_B.fasta
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| <!DOCTYPE HTML PUBLIC '-//W3C//DTD HTML 4.01 Transitional//EN'><html><head><META http-equiv='Content-Style-Type' content='text/css'><meta http-equiv='Content-Type' content='text/html; charset=ISO-8859-1'><title>GARD Results</title><LINK REL=STYLESHEET TYPE='text/css' HREF='http://www.datamonkey.org/GARD/styles/styles.css'></head><body><DIV CLASS = 'RepClassSM'>Processed alignment <b>/home/sbell23/gardB/lanl14_lesshiv_B.fasta</b> with 64 sequences and 3001 sites.<p> Processor time taken: 123275 seconds.</DIV><DIV class = 'RepClassSM'><u>Results</u><p><DIV class = 'RepClassSM'><b>GARD found evidence of 2 breakpoints</b><p><html><body><div style = 'width: 580px; border: black solid 1px; '><table style = 'width: 100%;font-size: 10px;text-align:left;'><tr><th>BPs</th><th>c-AIC</th><th>Δ c-AIC</th><th width = '70%'>Segments</th></tr> | ||
| <tr><td>0</td><td><div style = 'width: 100%; background-color: purple; color: white;'>221498.2064243095</div></td><td></td><td><table><tr><td style = 'font-size:10px;width: 406px;background-color:red; color:white'>1-3001</td></tr></table></td></tr> | ||
| <tr><td>1</td><td><div style = 'width: 99%; background-color: purple; color: white;'>220862.1268044667</div></td><td>636.0796198427852</td><td><table style = 'padding: 0px; spacing: 0px;'><tr><td style = 'width:206px; background-color: red; color: white; text-align: right; font-size: 10px;'>1526</td><td style = 'width:199px; background-color: black; color: white; text-align: right; font-size: 10px;'> </td></tr></table></td></tr> | ||
| <tr><td>2</td><td><div style = 'width: 99%; background-color: purple; color: white;'>220327.3870434978</div></td><td>534.7397609688342</td><td><table style = 'padding: 0px; spacing: 0px;'><tr><td style = 'width:132px; background-color: red; color: white; text-align: right; font-size: 10px;'>979</td><td style = 'width:83px; background-color: black; color: white; text-align: right; font-size: 10px;'>1598</td><td style = 'width:189px; background-color: blue; color: white; text-align: right; font-size: 10px;'> </td></tr></table></td></tr> | ||
| <tr><td>3</td><td><div style = 'width: 99%; background-color: purple; color: white;'>220327.3870434978</div></td><td>0</td><td><table style = 'padding: 0px; spacing: 0px;'><tr><td style = 'width:132px; background-color: red; color: white; text-align: right; font-size: 10px;'>979</td><td style = 'width:83px; background-color: black; color: white; text-align: right; font-size: 10px;'>1598</td><td style = 'width:189px; background-color: blue; color: white; text-align: right; font-size: 10px;'> </td></tr></table></td></tr> | ||
| </table></div></body></html></DIV> | ||
| </DIV><DIV CLASS='RepClassSM'><span class = 'font-variant:small-caps;'>Substitution process parameters</span><p><b>Nucleotide Model (012234) Fit Results</b><p>Log likelihood : <span style = 'position: absolute; left: 290px'>-110606.5976255626</span><br>c-AIC : <span style = 'position: absolute; left: 290px'>221498.2064243095</span><br><p>Using general discrete distribution of rates across sites<br> Rate : 0.049<span style = 'position: absolute; left: 290px'>Weight : 0.270</span><br> Rate : 0.622<span style = 'position: absolute; left: 290px'>Weight : 0.315</span><br> Rate : 1.905<span style = 'position: absolute; left: 290px'>Weight : 0.415</span><p><u>Nucleotide substitution rate matrix</u><p><TABLE><TR CLASS = 'TRReportT'><TH> </TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR><TR CLASS = 'TRReport1'><TH>A</TH><TD>*</TD><TD>0.4981053221974206</TD><TD>1</TD><TD>0.4313174416960855</TD></TR><TR CLASS = 'TRReport2'><TH>C</TH><TD>-</TD><TD>*</TD><TD>0.4313174416960855</TD><TD>1.500882306303908</TD></TR><TR CLASS = 'TRReport1'><TH>G</TH><TD>-</TD><TD>-</TD><TD>*</TD><TD>0.1315013308068441</TD></TR><TR CLASS = 'TRReport2'><TH>T</TH><TD>-</TD><TD>-</TD><TD>-</TD><TD>*</TD></TR></TABLE></DIV></html></body></html> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| inputRedirect = {}; | ||
|
|
||
| /* specify input alignment (full path) */ | ||
| inputRedirect["01"]="/home/sbell23/gardB/lanl14_lesshiv_B.fasta"; | ||
|
|
||
| /* specify nucleotide model (perhaps run NucModelCompare, or use GTR=012345 */ | ||
| inputRedirect["02"]="012234"; | ||
|
|
||
| /* site variation? General Discrete is recommended, but other options are None (fastest) or Beta-Gamma */ | ||
| inputRedirect["03"]="General Discrete"; | ||
|
|
||
| /* How many distribution bins [2-32]? (unless None was chosen for site variation, in which case do not use this input) */ | ||
| inputRedirect["04"]="3"; | ||
|
|
||
| /* specify what output files will be called - there will be four outputs, with this stem in the name (give full path, otherwise it'll end up in /home/jayoung/malik_lab_shared/linux_gizmo/lib/hyphy/TemplateBatchFiles) */ | ||
| inputRedirect["05"]="/home/sbell23/gardB/lanl14_lesshiv_B.fasta.GARD"; | ||
|
|
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| /* do the analysis */ | ||
| ExecuteAFile (HYPHY_BASE_DIRECTORY + DIRECTORY_SEPARATOR+"GARD.bf", inputRedirect); |
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